Large-scale Geometric Data Decomposition, Processing and Structured Mesh Generation

Mesh generation is a fundamental and critical problem in geometric data modeling and processing. In most scientific and engineering tasks that involve numerical computations and simulations on 2D/3D regions or on curved geometric objects, discretizing or approximating the geometric data using a polygonal or polyhedral meshes is always the first step of the procedure. The quality of this tessellation often dictates the subsequent computation accuracy, efficiency, and numerical stability. When compared with unstructured meshes, the structured meshes are favored in many scientific/engineering tasks due to their good properties. However, generating high-quality structured mesh remains challenging, especially for complex or large-scale geometric data. In industrial Computer-aided Design/Engineering (CAD/CAE) pipelines, the geometry processing to create a desirable structural mesh of the complex model is the most costly step. This step is semi-manual, and often takes up to several weeks to finish. Several technical challenges remains unsolved in existing structured mesh generation techniques. This dissertation studies the effective generation of structural mesh on large and complex geometric data. We study a general geometric computation paradigm to solve this problem via model partitioning and divide-and-conquer. To apply effective divide-and-conquer, we study two key technical components: the shape decomposition in the divide stage, and the structured meshing in the conquer stage. We test our algorithm on vairous data set, the results demonstrate the efficiency and effectiveness of our framework. The comparisons also show our algorithm outperforms existing partitioning methods in final meshing quality. We also show our pipeline scales up efficiently on HPC environment

Quality Improvements in Extruded Meshes Using Topologically Adaptive Generalized Elements

In this dissertation, a novel method to extrude near-body meshes from surface meshes of arbitrary topology that exploits topologically adaptive generalized elements to improve mesh quality is presented. Specifically, an advancing layer algorithm to generate near-body meshes which are appropriate for viscous fluid flows is discussed. First, an orthogonal two-layer algebraic reference mesh is generated. The reference mesh is then smoothed using a locally three-dimensional Poisson-type mesh generation equation that is generalized to smooth extruded meshes of arbitrary surface topology. Local quality improvement operations such as edge collapse, face refinement, and local reconnection are performed in each layer to drive the mesh toward isotropy. An automatic marching thickness reduction algorithm is used to extrude from multiple geometries in close proximity. A global face refinement algorithm is used to improve the transition from the extruded mesh to the voidilling tetrahedral mesh. A few example meshes along with quality plots are presented to demonstrate the efficacy of the algorithms developed

Frame Fields for Hexahedral Mesh Generation

As a discretized representation of the volumetric domain, hexahedral meshes have been a popular choice in computational engineering science and serve as one of the main mesh types in leading industrial software of relevance. The generation of high quality hexahedral meshes is extremely challenging because it is essentially an optimization problem involving multiple (conflicting) objectives, such as fidelity, element quality, and structural regularity. Various hexahedral meshing methods have been proposed in past decades, attempting to solve the problem from different perspectives. Unfortunately, algorithmic hexahedral meshing with guarantees of robustness and quality remains unsolved. The frame field based hexahedral meshing method is the most promising approach that is capable of automatically generating hexahedral meshes of high quality, but unfortunately, it suffers from several robustness issues. Field based hexahedral meshing follows the idea of integer-grid maps, which pull back the Cartesian hexahedral grid formed by integer isoplanes from a parametric domain to a surface-conforming hexahedral mesh of the input object. Since directly optimizing for a high quality integer-grid map is mathematically challenging, the construction is usually split into two steps: (1) generation of a feature-aligned frame field and (2) generation of an integer-grid map that best aligns with the frame field. The main robustness issue stems from the fact that smooth frame fields frequently exhibit singularity graphs that are inappropriate for hexahedral meshing and induce heavily degenerate integer-grid maps. The thesis aims at analyzing the gap between the topologies of frame fields and hexahedral meshes and developing algorithms to realize a more robust field based hexahedral mesh generation. The first contribution of this work is an enumeration of all local configurations that exist in hexahedral meshes with bounded edge valence and a generalization of the Hopf-Poincaré formula to octahedral (orthonormal frame) fields, leading to necessary local and global conditions for the hex-meshability of an octahedral field in terms of its singularity graph. The second contribution is a novel algorithm to generate octahedral fields with prescribed hex-meshable singularity graphs, which requires the solution of a large non-linear mixed-integer algebraic system. This algorithm is an important step toward robust automatic hexahedral meshing since it enables the generation of a hex-meshable octahedral field. In the collaboration work with colleagues [BRK+22], the dataset HexMe consisting of practically relevant models with feature tags is set up, allowing a fair evaluation for practical hexahedral mesh generation algorithms. The extendable and mutable dataset remains valuable as hexahedral meshing algorithms develop. The results of the standard field based hexahedral meshing algorithms on the HexMesh dataset expose the fragility of the automatic pipeline. The major contribution of this thesis improves the robustness of the automatic field based hexahedral meshing by guaranteeing local meshability of general feature aligned smooth frame fields. We derive conditions on the meshability of frame fields when feature constraints are considered, and describe an algorithm to automatically turn a given non-meshable frame field into a similar but locally meshable one. Despite the fact that local meshability is only a necessary but not sufficient condition for the stronger requirement of meshability, our algorithm increases the 2% success rate of generating valid integer-grid maps with state-of-the-art methods to 57%, when compared on the challenging HexMe dataset

Combinatorial meshing for mechanical FEM

Diese Dissertation führt die Forschung zur Erzeugung von FEM Netzen für mechanische Simulationen fort. Zur zielgerichteten Steuerung der weiteren Forschung in diesem Feld wurde eine Umfrage zur Identifikation der Kerninteressen der Anwender durchgef¨uhrt. Das vorgestellte Verfahren des Combinatorial Meshing ist ein neuartiges Konzept im Bereich Grid Based Meshing. Im Gegensatz zu den kartesischen Gittern, die im Grid Based Meshing Anwendung finden wird ein an das Problem angepasstes Gitter genutzt. Dieses Precursor Mesh wird durch Analyse des CAD Strukturbaums der Geometrie gewählt. Die Zellen des Precursor Mesh werden mit vorberechneten Netzsegmenten – sogenannten Superelementen gefüllt. Die Wahl passender Superelemente wird als combinatorisches Optimierungsproblem modelliert. Dieses wird mit Hilfe von Answer Set Programming (ASP) und einem alternativen heuristischen Ansatz gelöst. Beide Verfahren werden in Hinblick auf Zeitkomplexität und Ergebnisqualität verglichen. Das resultierende Netz ist eine Grobe Näherung der Zielgeometrie, die an geometrische Elemente angebunden werden muss. Für diesen Prozess wird ein neuer Algorithmus vorgestellt, der automatisch identifizieren kann, an welche Geometrieelemente Oberflächenknoten des Netzes gebunden werden müssen um die Zielgeometrie möglichst exakt abzubilden. Für die Erzeugung der Superelemente wird ein neues Verfahren auf Basis von ASP entwickelt. Um die Generierung von FEM Netzen mit ASP zu ermöglichen, wird das Problem der Netzgenerierung als graphentheoretisches Problem modelliert. Dieses ist die Wahl eines optimalen Subgraphen aus einem Primärgraph. Dieses Problem wird mit einem ASP Solver für verschiedene Optimierungsziele gelöst. Die Graphenformulierung ist zudem ein Fortschritt im theoretischen Verständnis der Komplexität der Netzgenerierung.his dissertation advances the research of mesh generation for Finite Element Method simulation for mechanical applications. In order to target further research at user needs, a survey is conducted to identify the most pressing issues in FEM software. The concept of Combinatorial Meshing is proposed as a novel approach to grid based meshing. While conventional grid based meshing works on trivial Cartesian grids, the use of a Precursor Mesh instead of a grid is proposed. Appropriate Precursor Meshes are selected by analyzing the internal feature structure of the provided CAD data. The cells of this Precursor Mesh are then filled with precomputed mesh templates – called Super Elements. The selection of appropriate Super Elements is modeled as a combinatorial optimization problem. To solve this problem, Answer Set programming (ASP) and a heuristic approach are compared with respect to their time complexity and result quality. The resulting mesh is a rough approximation of the target geometry which then has to be fitted to the geometric entities. For this process a novel algorithm is presented which is able to automatically identify the geometric entities on which the surface nodes of the mesh have to be drawn in order to generate high quality meshes and correctly approximate the desired geometry. For the generation of Super Element Meshes, a novel approach based on ASP is developed. In order to enable meshing with ASP, a graph representation of a mesh is developed and the meshing process is formulated as a graph selection problem. It is then solved with an ASP solver for multiple optimization goals. The graph formulation will also aid the theoretical understanding of meshing complexity

ICASE/LaRC Workshop on Adaptive Grid Methods

Solution-adaptive grid techniques are essential to the attainment of practical, user friendly, computational fluid dynamics (CFD) applications. In this three-day workshop, experts gathered together to describe state-of-the-art methods in solution-adaptive grid refinement, analysis, and implementation; to assess the current practice; and to discuss future needs and directions for research. This was accomplished through a series of invited and contributed papers. The workshop focused on a set of two-dimensional test cases designed by the organizers to aid in assessing the current state of development of adaptive grid technology. In addition, a panel of experts from universities, industry, and government research laboratories discussed their views of needs and future directions in this field

Efficient matrix-free implementation and automated verification of hybridizable discontinuous Galerkin finite element methods

This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Thesis: S.M., Massachusetts Institute of Technology, Department of Mechanical Engineering, 2019Cataloged from PDF version of thesis.Includes bibliographical references (pages 93-99).This work focuses on developing efficient and robust implementation methods for hybridizable discontinuous Galerkin (HDG) schemes for fluid and ocean dynamics. In the first part, we compare choices in weak formulations and their numerical consequences. We address details in making the leap from the mathematical formulation to the implementation, including the different spaces and mappings, discretization of the integral operators, boundary conditions, and assembly of the linear systems. We provide a flexible mapping procedure amenable to both quadrature-free and quadrature-based discretizations, and compare the accuracy of the two on different problem geometries. We verify the quadrature-free approach, demonstrating that optimal orders of convergence can be obtained, even on non-affine and curvilinear geometries. The second part of the work investigates the scalability of HDG schemes, identifying memory and time-to-solution bottlenecks. The form of the quadrature-free integral operators is exploited to develop a novel and efficient matrix-free approach to solving the global linear system that arises from HDG discretizations. Additional manipulations to improve numerical robustness are discussed. To mitigate the complexity of the implementation, we provide an automated and computationally efficient verification procedure for the HDG methodologies discussed, using a hierarchical approach to provide diagnostic information and isolate problems. Finally, challenges related to the effective visualization of high-order, discontinuous HDG-FEM data for fluid and ocean applications are illustrated and strategies are provided to address them.by Corbin Foucart.S.M.S.M. Massachusetts Institute of Technology, Department of Mechanical Engineerin

A fast and robust patient specific Finite Element mesh registration technique: application to 60 clinical cases

Finite Element mesh generation remains an important issue for patient specific biomechanical modeling. While some techniques make automatic mesh generation possible, in most cases, manual mesh generation is preferred for better control over the sub-domain representation, element type, layout and refinement that it provides. Yet, this option is time consuming and not suited for intraoperative situations where model generation and computation time is critical. To overcome this problem we propose a fast and automatic mesh generation technique based on the elastic registration of a generic mesh to the specific target organ in conjunction with element regularity and quality correction. This Mesh-Match-and-Repair (MMRep) approach combines control over the mesh structure along with fast and robust meshing capabilities, even in situations where only partial organ geometry is available. The technique was successfully tested on a database of 5 pre-operatively acquired complete femora CT scans, 5 femoral heads partially digitized at intraoperative stage, and 50 CT volumes of patients' heads. The MMRep algorithm succeeded in all 60 cases, yielding for each patient a hex-dominant, Atlas based, Finite Element mesh with submillimetric surface representation accuracy, directly exploitable within a commercial FE software

Flow through and around fish farming nets

Computational fluid dynamics (CFD) modeling, tow tank and field measurements were used to investigate current flow through and around net panels and cages. For the numerical computations a porous media model was used to represent the net allowing efficient computation of both exterior and interior flow fields. The model was calibrated using tow tank measurements on a net panel at different velocities and angles of attack. The CFD method was able to reproduce the drag- and lift coefficients of the net panel and the velocity reduction behind the net panel with satisfactory accuracy. The approach was validated for a small size gravity cage by comparing CFD predictions with tow tank measurements of drag force on the cage and velocity reduction inside the cage and in the wake region. The modeled drag force was higher than the measured drag force. The modeled current compared well with the measured current inside the cage, but the reduction was underpredicted in the wake of the cage. Full scale simulations were performed for a cage with a clean net and a biofouled net and compared with field measurements of a cage fouled with jellyfish. The measured data compared well with model predictions for the biofouled net. Flushing rates were calculated for both the clean and the biofouled net cases. When the net was changed from clean to biofouled, flushing time increased by up to 44% and drag force increased by up to 80%